bowtie

Genetics

Software Description

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).


Info

Module Name

bowtie

Last Updated On

10/23/2023

Support Level

Secondary Support

Software Access Level

Open Access

Home Page

http://bowtie-bio.sourceforge.net/index.shtml

Documentation

Software Description

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

General Linux

To run this software interactively in a Linux environment run the commands:

module load bowtie
bowtie ...

For bowtie versions 2.0 and above, use the program "bowtie2" instead of simply "bowtie".

To see a list of available options, type the command

bowtie2 -h

Pre-built bowtie indexes for popular genomes are available at

/project/db/genomes/[species]/[build]/bowtie2

Bowtie programs may also be submitted to a queue using PBS script such as the one below:

#PBS -l nodes=3:ppn=8,pmem=1000mb,walltime=8:00:00
#PBS -m abe
#PBS -M sample_email@umn.edu

module load bowtie

bowtie2 -p $PBS_NP reads/e_coli_10000snp.fq ec_snp.sam

Note the use of -p $PBS_NP; this option is used to specify the number of threads used by Bowtie. Also note that only 0.X versions of Bowtie are available on Itasca and Cascade.

Compatibility issues: Bowtie genome indexes built using 0.X versions are not compatible with indexes built using 2.X versions. Significant changes (improvements) have been made to Bowtie command-line options, and to how Bowtie performs alignments. To see a list of installed Bowtie versions type the command

module show bowtie

Bowtie 0.X genome indexes are available at

/project/db/genomes/[SPECIES]/[BUILD]/bowtie

Agate Modules

Default

2.3.4.1

Other Modules

1.1.2, 2.1.0, 2.2.2, 2.2.4, 2.3.0, 2.3.1, 2.3.2, 2.3.4.1, 2.4.4

Mangi Modules

Default

2.3.4.1

Other Modules

1.1.2, 2.1.0, 2.2.2, 2.2.4, 2.3.0, 2.3.1, 2.3.2, 2.3.4.1, 2.4.4

Mesabi Modules

Default

2.3.4.1

Other Modules

1.1.2, 2.1.0, 2.2.2, 2.2.4, 2.3.0, 2.3.1, 2.3.2, 2.3.4.1, 2.4.4